You do not need to start/stop build server. TeamCity will detect the change automatically. Note, you should not open build configuration parameter setting from the web UI afterwards. Try running the build with patched parameters. Will it start x64 NCover? Please attach files from TeamCity.NET folder.

Yes. It will reswap parameters back. I'll added the fix to 5.1.x and 6.x branches. It will be available in 5.1.4. Let me know if you need patch faster. Please check NCover reporter arguments if you see no build log. TeamCity generates index.html file that enumerates all .html files in the folder if there was no index.html file found in the report generation folder.